FILE -In this July 9, 2010 file photo, UC Davis research scientist Marion Wittmann holds a handful of Asian clams removed from the bottom of the lake in 15-feet of water near South Lake Tahoe, Calif. After decades of delay, government officials are beginning to crack down on cargo ships that allow foreign invasive species to hitchhike to U.S. waters, where they have turned ecosystems upside down and caused billions in economic losses.

TRAVERSE CITY, Mich. — After decades of delay, government officials are beginning to crack down on cargo ships that allow foreign invasive species to hitchhike to U.S. waters, where they have turned ecosystems upside down and caused billions of dollars in economic losses.

Organisms as large as adult fish and as small as bacteria lurk in ship ballast tanks, which hold millions of gallons of water and sediments that keep vessels upright in rough seas. When the soupy mixtures are dumped in harbors as freight is taken on, the stowaways often find hospitable surroundings and no natural predators. They spread rapidly, starving out native species and spreading diseases in aquatic life.

Since arriving in the Great Lakes in the mid-1980s, the zebra mussel and its cousin the quagga mussel have clogged municipal and power plant water intake pipes. They're blamed for a Lake Huron salmon collapse and botulism that has killed thousands of shore birds. In San Francisco Bay, biologists say the Asian clam likely caused a decline of striped bass and other competitors for plankton.

Japanese shore crabs are threatening native clams and mussels from Maine to Chesapeake Bay, which is infested with 150-plus exotic species. Another invader, the spotted jellyfish, became so abundant in the Gulf of Mexico a decade ago they ripped apart fishing nets and caused a temporary halt to commercial shrimping.

"Larvae of almost every major group of invertebrates can be found in ballast water," said Tom Shirley, specialist with Texas A&M University-Corpus Christi. "Protozoa and bacteria thrive there, too."

Ballast is the biggest means of transport for the aquatic aliens, scientists say. Yet regulators have been slow to demand accountability from the shipping industry, which has long insisted there isn't adequate technology to make ballast tanks invader-free.

Now, agencies are turning up the heat as companies report progress toward developing effective sterilization systems. The U.S. Coast Guard says it will release final regulations by April limiting the number of live organisms in ballast water and let shippers decide how to comply.

The Environmental Protection Agency also has begun regulating discharges of ballast and other wastewater from vessels, although shippers and environmentalists sued. EPA is discussing settlements while crafting an updated discharge permit effective in 2013.

At least a dozen states also have ballast policies, leaving shippers increasingly worried about having to navigate a patchwork of requirements.

Industry groups contend a New York measure scheduled to take effect next year could bring traffic to a standstill on some of the nation's busiest waterways.

"You'll see the closure of the St. Lawrence Seaway," said Steve Fisher, executive director of the American Great Lakes Ports Association. "It would shut down about 50 percent of Great Lakes shipping and about all shipping in New York waters, including the Hudson River and the port of New York and New Jersey."

Jim Tierney, an executive in the New York Department of Environmental Conservation, said the agency was considering shippers' pleas for a grace period. Environmental groups want the department to stand its ground, pointing to findings by the National Oceanic and Atmospheric Administration that about 75 species are prime candidates to invade the Great Lakes, mostly through ballast water.

"Most clean-water laws assume it's OK to have a little pollution because it will dilute, evaporate, degrade," said Andy Buchsbaum, director of the National Wildlife Federation's office in Ann Arbor. "But invasive species are not like normal pollution. They reproduce and multiply. You have to keep the numbers as low as you possibly can to avoid reaching that critical mass where an entire water body will be colonized."

Since 2004, ships from overseas have been required to dump and replace ballast water, or rinse empty tanks, at least 200 miles from U.S. waters. But studies show that up to 30 percent of organisms remain alive in the tanks, said Andrew Cohen, director of the Center for Research on Aquatic Bioinvasions in Richmond, Calif.

"It's a pretty weak approach," Cohen said.

Researchers have spent years developing methods of sanitizing ballast with ultraviolet light, chemicals, filters and even oxygen depletion.

A first draft of the Coast Guard regulations would adopt international limits on numbers of organisms per cubic meter of ballast water.

The ceilings would take effect next year for new vessels and be phased in over several years for existing ones. A second set of limits about 1,000 times stronger in establishing limits per cubic meter of ballast water would be imposed later if studies show that could be accomplished.

Environmentalists are pushing for a quicker timetable, while shippers want it lengthened.

Cmdr. Gary Croot, chief of the Coast Guard's Environmental Standards Division, said the final rules being released this spring will reflect public feedback. "We certainly don't want to establish a standard that no one can comply with," he said.

New York's standard, which takes effect in 2012, would be 100 times more stringent than the proposed Coast Guard limit on organisms. California has adopted even tougher standards, but regulators say enforcement may be delayed.

"There have been ship owners ready and willing to make investments in ballast water treatment technology who have held back because they don't want to spend a million dollars on some system that may have to be ripped out in five years because it doesn't meet the standards," said Jennifer Carpenter, senior vice present of American Waterways Operators, an industry trade group.

EPA and the Coast Guard have commissioned studies to determine which standards and technology would work best. The number of live organisms permitted under the Coast Guard's draft policy is the equivalent of one drop of water in 20 Olympic-sized swimming pools, Croot said. Going significantly beyond that would be harder and costlier.

"If you want to make a car perfectly safe, conceivably that could be done, but at what expense?" Croot said.